X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=examples%2FappletParameters.html;h=04cc235164ee30368f32b1253282173f3a7016d5;hb=refs%2Fheads%2Ffeatures%2FJAL-4219_extended_fasta_rna_ss;hp=433f5a917f926b4ba361001be86b2a7fb721b813;hpb=62908e93f175753769436fd62193773b9f3ad26f;p=jalview.git diff --git a/examples/appletParameters.html b/examples/appletParameters.html index 433f5a9..04cc235 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -28,7 +28,7 @@ which are described below. Once initialised, the applet can be interacted with via its Javascript API.
Issues arising from tightening of Java Security default settings
JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java may not be compatible with these settings.
For additional deployment notes, see below.
+For additional deployment notes, see Applet Deployment.
jnetfile | fileName | Secondary structure predictions from a Jnet Concise - file will be added to the first sequence in the alignment. | + href="http://www.compbio.dundee.ac.uk/~www-jpred/">JPred Concise + file will be added to the first sequence in the alignment.|
PDBfile(x) | @@ -114,7 +115,7 @@ the applet can be interacted with via itsdefaultColour | One of: Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix - Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices |
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, T-Coffee Scores, RNA Helices
Default is no colour. |
Default is true. | |||
showOccupancy | +true or false | +Default is true. | +|
sortBy | Id , Pairwise Identity, or Length | Sorts the alignment on startup |